Donations are already taxed for most non-profits. Tax-exemption for donations isn't the same thing as not paying a corporate tax. Bear in mind that it is trivial to set up non-profit organizations and easy-peasy to use them to pass absolutely obscene not-profits straight through to the corporate officers as salaries, who just happen to be the folks that founded the not-for-profit and who own its not-for-profit shares that, in the event that those same officer/owners convert it over to for-profit, will become disgustingly valuable in an instant (see the history of Blue-Cross-Blue-Shield, for example). My wife worked for just such a non-profit until about a year ago. The company president of this not-for-profit company was knocking down seven digit salaries plus seven digit bonuses at the same time they were cutting her income to pay for an IT transition that they mandated. Her "donation" to the company was indeed not taxed -- it wasn't even voluntary. Non-profits need substantial tax revision almost as badly as religions.
You seem confused about the constitution, the bill of rights, and taxation in general, and nobody has suggested taxing people for exercising a civil liberty (certainly not me). What is being suggested is not giving people a tax deduction for money donated to a club. I'd oppose giving a tax deduction for dues paid to the Shriners, the Benevolent and Paternal Order of the Elks, the Masons, the Knights of Columbus, etc on the same basis, even though in some cases some of those organizations do some charitable works some of the time. I'm even borderline comfortable with tax breaks for donations to things like the Salvation Army whose primary focus is charity, although I am most unhappy with the way they pay their corporate officers and don't like the idea that those that they help get the help only at the cost of proselytizing. I could see clear to similar rules for genuine charities stripped of the missionary component set up by religious groups as well.
But the pass-the-hat donations to churches, used primarily to pay to maintain the infrastructure and personnel of the church, no. Taxing that isn't taxing your right to exercise a civil liberty -- nothing in the world is preventing you from belief or worship. It is taxing the money you are giving to a club designed to promote your belief in yourself and others and to support a huge formal infrastructure that yes, absolutely, exercises a substantial amount of power. We have similar laws regulating donations to things like political action committees and candidates for office -- if those laws were fairly applied to many churches they would not meet the criteria for 527 status because they often advocate for specific candidates or positions and are knee-deep in issue advocacy.
Some churches do good stuff some of the time. My niece is a Methodist minister; so was my grandfather. My grandfather, from all accounts, was a sharpster who ran his household until he ran out of money and then went and held a tent revival somewhere to refill his coffers. My niece works in Palestine trying to bring justice for the Palestinians and peace in a land that has almost never known it. But if you donate money to the Methodist church in church, almost all of that money goes to support the church itself and the minister that preaches to you on Sunday. That's the money I don't think should be deductible, because the government has no business subsidizing the support of churches, synagogues, mosques, temples, or the people that run them, "cult" or not, and tax breaks are a de-facto subsidy.
If at some time you want to talk about the religious beliefs or lack thereof of our founding fathers, I'm happy to direct you to their own writings in which it was made perfectly clear that most of them were anything from atheists to deists. Jefferson's personal ambition was to establish a state free from religion, not a religious state, a state where one did not have to profess belief in a God at all in order to exercise political rights.
If you look up above, you can see precisely where that plan has been run awry by your own words. You are quite right. Even for atheists like Abraham Lincoln and Jefferson and John Adams and George Washington and Thomas Paine, it was necessary to hide their (lack of) beliefs in a world where political power was solidly in the grasp of the churches. It still is. One cannot get elected as an atheist. Which all by itself says that something has gone very, very wrong with the founding fathers' ideal of religious freedom -- freedom from religion, especially in politics. All you are doing is confirming my reasons for wanting to oppose it -- you suggest that anybody "godless" must be "totalitarian" (bullshit!) or that simply actually enforcing the separation of church and state that the bill of rights requires and getting nonsense like "In God we Trust" off of our currency is somehow threatening to our civil liberties rather than actively enforcing them.
I really do suggest that you consider studying the Bible before you suggest that our rights were endowed by a Creator. The Bible makes it clear that humans have no rights whatsoever. For example, it explains that I can beat my slaves almost to death, or rape my neighbor's daughter as long as I pay her father 20 shekels of silver afterwards and marry her. Numbers 21 is another really excellent passage describing the genocidal slaughter of women, children and old men except for the young virgin women in the Midianite crowd who were given to the troops to rape and enslave as part of the booty -- by Moses, who was surely a righteous man, somebody Jesus was perfectly happy to walk around with up on the mount. Consider that at no time in the history of the world has God enforced a single human right. No injustice, no matter how it cries out to the sky for correction, has ever been repaired by a divine act. Every day acts of unspeakable horror occur -- plenty of them as the result of so-called acts of God -- without any hint of divine rescue or retribution.
No, human rights were invented by humans -- in particular by Thomas Hobbes, John Locke, and Thomas Jefferson, especially by Jefferson who gave them a compelling poetic appeal, one that could rouse passion in the human heart. The declaration of independence is a statement of what the world should have been if God had in fact been on the job, and an acknowledgement that since he's not, since there is no such thing, it is high time that we as human beings pick up the burden for ourselves. If you want heaven, if you want justice, you'd better put your shoulder to the wheel and make it happen here on Earth because there is no divine heaven or hell or cosmic justice before, during, or afterward.
I can do no better than close with a nice quote from Thomas Paine, one of our good old founding fathers:
All national institutions of churches, whether Jewish, Christian or Turkish, appear to me no other than human inventions, set up to terrify and enslave mankind, and monopolize power and profit.
That, my friend, is the common attitude of the founding fathers, most of whom were sufficiently adept at concealing the depth of their antipathy to organized religion that they could continue to hold political power in a world where mankind was already enslaved, where the church(es) already held the monopoly on profit and power. It has taken hundreds of years to break that monopoly. The work isn't finished yet. But the age of reason that Paine called for is gradually bringing it about, because -- and I know you won't like this, but it is simple truth and you should think about it -- reason and religion are fundamentally incompatible. You cannot consistently accept a dual standard for determining probable truth, one for "scientific" facts deduced using observation and consistently applied reason in the actual world and another for "truths" supposedly stated by people whose primary goal was the establishment of a stable religious hegemony that conferred upon them substantial power and wealth and tribal status, which have no observational basis and which cannot ever be verified or disproven by observation or reason.
That's why you are reduced to making up stuff about Creators and trying to tie it into what might have caused the Big Bang or other observed aspects of the visible Universe. Nobody can prove you wrong, to be sure. You could assert that the big bang was the hatching of a giant egg (Hindu), or the expression of certain bodily fluids (Greek) or that it can be mapped in some improbable way into the absurdities at the beginning of Genesis and nobody can possibly prove you wrong. In fact, you can make up a literally infinite number of stories for what might have gone on beforehand. You can support them by means of antique scriptures or just invent them. There really isn't any difference.
Physicists (I am a physicist, BTW) do the same thing -- they try to imagine what might have been going on beforehand. The difference is that their guesses and imagination are tempered by the need for absolute, rigorous consistency with the body of knowledge we have gradually built up that can be verified at any time by any person interested in doing so by the means of performing various experiments or observations, and that physicists do not assert their hypotheses as truth . Physical laws are expressed as probable truth -- in the case of some things, very, very probable truth -- but we always maintain the mental flexibility to change our minds in the event that an experiment comes along that disproves a belief or demonstrates that the belief is not complete.
Where is there any evidence of that rational process in religion? Physics is humble and skeptical where religion is arrogant and certain. In science there is no revealed truth, only truth as we can best discern it when we work very hard and in a completely open and collaborative way. In religion it is exactly the opposite -- all truth is revealed truth, and (with the exception of perhaps the Quakers) such truths are held to be immutable and unchallengable. For most of human history, to openly challenge a supposed revealed truth was to invite torture and death.
You like the idea of freedom. So do I. And the most basic freedom is the freedom to think, to challenge the system of beliefs you were force-fed as a child and indoctrinated in to the point where you find it difficult to challenge them. I suggest that you use it.